Hotspots API: A Python Package for the Detection of Small Molecule Binding Hotspots and Application to Structure-Based Drug Design.

08:00 EDT 24th March 2020 | BioPortfolio

Summary of "Hotspots API: A Python Package for the Detection of Small Molecule Binding Hotspots and Application to Structure-Based Drug Design."

Methods that survey protein surfaces for binding hotspots can help to evaluate tar-get tractability and guide exploration of potential ligand binding regions. Fragment Hotspot Maps builds upon interaction data mined from the CSD (Cambridge Structural Database) and exploits the idea of identifying hotspots using small chemical fragments, which is now widely used to design new drug leads. Prior to this publication, Fragment Hotspot Maps was only publicly available through a web application.To increase the accessibility of this algorithm we present the Hotspots API (Application Programming Interface), a toolkit that offers programmatic access to the core Fragment Hotspot Maps algorithm, thereby facilitating the interpretation and application of the analysis. To demonstrate the package's utility, we present a workflow which automatically derives protein hydrogen-bond constraints for molecular docking with GOLD. The Hotspots API is available from,, under the MIT license and is dependent upon the commercial CSD Python API.


Journal Details

This article was published in the following journal.

Name: Journal of chemical information and modeling
ISSN: 1549-960X


DeepDyve research library

PubMed Articles [17692 Associated PubMed Articles listed on BioPortfolio]

Neuronal Cytoskeleton: Presynaptic Boutons as Hotspots for Activity-Dependent Microtubule Nucleation.

Local microtubule remodeling plays a crucial role in controlling the transport of neuronal cargo. A new study reveals that excitatory en passant boutons in the axon are hotspots for activity-induced m...

Snake recombination landscapes are concentrated in functional regions despite PRDM9.

Meiotic recombination in vertebrates is concentrated in hotspots throughout the genome. The location and stability of hotspots have been linked to the presence or absence of PRDM9, leading to two prim...

Characterization of sequence variability hotspots in Cranichideae plastomes (Orchidaceae, Orchidoideae).

This study reports complete plastome sequences for six species of Neotropical Cranichideae and focuses on identification of the most variable regions (hotspots) in this group of orchids. These structu...

Conserved HORMA domain-containing protein Hop1 stabilizes interaction between proteins of meiotic DNA break hotspots and chromosome axis.

HORMA domain-containing proteins such as Hop1 play crucial regulatory roles in various chromosomal functions. Here, we investigated roles of the fission yeast Hop1 in the formation of recombination-in...

Twists or turns: stabilising alpha beta turns in tetrapeptides.

Protein-protein interactions involve hotspots as small as 4 sequential amino acids. Corresponding tetrapeptides have no structure in water. Here we report linking side chains of amino acids X and Z to...

Clinical Trials [7454 Associated Clinical Trials listed on BioPortfolio]

EMA for Tobacco Control Policy Research

The study aims to (1) evaluate the effectiveness of the recent renewal of tobacco health warnings (HWs) on noticing and anti-smoking responses, and (2) assess the effect of exposure to poi...

PMCAN for Smokers at Smoking Hotspots: a Pilot RCT

Background: Many smokers cannot quit due to nicotine withdrawal symptoms, which peak at the first week of abstinence. Proactive recruitment of smokers is needed as most smokers do not seek...

Glucose Metabolic, Amyloid, and Tau Brain Imaging in Down Syndrome and Dementia

The purpose of this study is to develop small molecule radio-labeled probes of beta-amyloid, to be used with positron emission tomography (PET) for early detection and treatment monitoring...

Amyloid Plaque and Tangle Imaging in Alzheimer's Disease and Down Syndrome

The purpose of this study is to develop small molecule radio-labeled probes of beta-amyloid, to be used with positron emission tomography (PET) for early detection and treatment monitoring...

Effectiveness of Mass Drug Administration for Reducing Seasonal Malaria Transmission in Zanzibar

The overall aim of this study is to determine the effectiveness of two rounds of mass drug administration (MDA) with dihydroartemisinin-piperaquine (DHAp) + single low dose (SLD) primaquin...

Medical and Biotech [MESH] Definitions

A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)

Part of a MESSENGER RNA molecule that undergoes a conformation change upon binding a specific metabolite or other small molecule thereby regulating the messenger RNA's transcription, post-transcriptional processing, transport, translation, or stability in response to varying levels of the metabolite or other small molecule.

A small cytosolic fatty-acid binding protein that forms a lipid-binding beta-barrel structure and is expressed by CARDIOMYOCYTES and at lower levels in brain tissue. It is released into plasma immediately following cardiac injury and may therefore serve as a useful biomarker for the early detection of MYOCARDIAL INFARCTION.

Detection of drugs that have been abused, overused, or misused, including legal and illegal drugs. Urine screening is the usual method of detection.

The small ribonucleoprotein component of RIBOSOMES. It contains the MESSENGER RNA binding site and two TRANSFER RNA binding sites - one for the incoming AMINO ACYL TRNA (A site) and the other (P site) for the peptidyl tRNA carrying the elongating peptide chain.

Quick Search

DeepDyve research library

Relevant Topic

Pharmacy is the science and technique of preparing as well as dispensing drugs and medicines. It is a health profession that links health sciences with chemical sciences and aims to ensure the safe and effective use of pharmaceutical drugs. The scope of...

Searches Linking to this Article